Publications

 

Journal Papers

13. Jinkyung Kim, Feng Luo, and Xiuping Jiang. Factors Impacting the Regrowth of Escherichia coli O157:H7 in Dairy Manure Compost. Journal of Food Protection, Volume 72, Number 7, July 2009, pp. 1576-1584.

12. Feng Luo*, Bo Li, Xiu-Feng Wan, Richard H. Scheuermann. Core and periphery structures in protein interaction networks. BMC Bioinformatics 2009, 10 (Suppl 4):S8 (Extension of BIBM 2008 paper).

 

11. Yunfeng Yang, Daniel P. Harris, Feng Luo, Marcin Joachimiak, Liyou Wu, Paramvir Dehal, Janet Jacobsen, Zamin Yang, Haichun Gao, Adam P. Arkin, Anthony V. Palumbo and Jizhong Zhou. Snapshot of Iron Response in Shewanella oneidensis by Gene Network Reconstruction. BMC Genomics, 2009, 10:131.

 

10. Xiu-Feng Wan, Tung Nguyen, C. Todd Davis, Catherine B. Smith, Zi-Ming Zhao, Margaret Carrel, Kenjiro Inui, Hoa T. Do, Duong T. Mai, Samadhan Jadhao, Amanda Balish, Feng Luo, Michael Emch, Yumiko Matsuoka, Nancy J. Cox, Cam V. Nguyen, Alexander Klimov, and Ruben O. Donis. Evolution of Highly Pathogenic H5N1 Avian Influenza Viruses in Vietnam between 2001 and 2007: Introduction, Reassortment, and Emergence of Novel Genotypes. PLOS One, 2008, 3(10): e3462.

 

9. Feng Luo*, James Z. Wang, Eric Promislow. Exploring Local Community Structures in Large Networks. Web Intelligence and Agent Systems, volume 6, Number 4, 387-400, 2008, IOS Press.

 

8. Yunfeng Yang, Daniel P. Harris, Feng Luo, Liyou Wu, Andrea B. Parsons, Anthony V. Palumbo and Jizhong Zhou. Characterization of the Shewanella oneidensis Fur Gene: Roles in Iron and Acid Tolerance Response. BMC Genomics, 2008; 9, Supplement 1:S11. (Extension of BioComp 2007 paper).

 

7. Xiu-Feng Wan, Guorong Chen, Feng Luo, Michael Emch and Ruben Donis, A Quantitative Genotype Algorithm Reflecting H5N1 Avian Influenza Niches. Bioinformatics, 23(18):2368-2375, 2007.

 

6. Feng Luo, Yunfeng Yang, Jianxin Zhong, Haichun Gao, Latifur Khan, Dorothea K. Thompson, Jizhong Zhou. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinformatics 2007, 8:299.

 

5. Feng Luo*, Yunfeng Yang, Chin-Fu Chen, Roger Chang, Jizhong Zhou, Richard Scheuermann. Modular Organization of Protein Interaction Network. Bioinformatics, 23(2): 207-214, 2007.

 

4. Feng Luo, Jianxin Zhong, Yunfeng Yang, Richard Scheuermann, Jizhong Zhou. Application of Random Matrix Theory to Biological Networks. Physics Letters A, Volume 357, Issue 6, 420-423, 2006.

 

3. Feng Luo, Yunfeng Yang, Jianxin Zhong, Jizhong Zhou. Application of Random Matrix Theory to Microarray Data for Discovering Functional Gene Modules. Physical Review E, 73, 031924, 2006.

 

2. Latifur Khan, Feng Luo. Hierarchical Clustering of Complex Data. Special issue of International Journal on Artificial Intelligence Tools, Vol. 14, No. 5, 791-809, 2005.

 

1. Feng Luo, Latifur Khan, I-Ling Yen, Farokh Bastani, Jizhong Zhou. A Dynamical Growing Self-Organizing Tree (DGSOT) For Hierarchical Clustering Gene Expression Profiles. Bioinformatics, Volume 20, Issue 16, 2605-2617, 2004.

 

Book Chapter

 

1. Feng Luo, Latifur Khan. Data complexity in clustering analysis of gene microarray expression profiles. in Complexity in Pattern Recognition, Edited by Dr. Mitra Basu and Dr. Tin Kam Ho, Springer Verlag, 2006.

 

Refereed Conference Papers

 

8. Feng Luo*, Thomas Grindinger, Xiu-Feng Wan, Richard H. Scheuermann. Exploring core/periphery structures in protein interaction networks provides structure-property relation insights. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia, PA, November, 2008. (accepted rate 24.4%).

 

7. Roger L. Chang, Feng Luo, Stuart Johnson and Richard H. Scheuermann. Deterministic Graph-Theoretic Algorithm for Detecting Modules in Biological Interaction Networks. The 5th Annual Biotechnology and Bioinformatics Symposium (BIOT-2008), 1-10, Arlington, Texas, October, 2008.

 

6. Yunfeng Yang, Daniel P. Harris, Feng Luo, Liyou Wu, Andrea B. Parsons, Anthony V. Palumbo and Jizhong Zhou. Physiological and Transcriptomic Analyses to Characterize the Function of Fur and Iron Response in Shewanella oneidensis. The 2007 International Conference on Bioinformatics & Computational Biology (BioComp 2007), 707-713,  Monte Carlo Resort, Las Vegas, Nevada, June, 2007.

 

5. Feng Luo*, James Z. Wang, Eric Promislow. Exploring Local Community Structures in Large Networks. IEEE /WIC/ACM International Conference on Web Intelligence (WI 2006), 233-239, Hong Kong, China, December, 2006. (accept rate 18% for regular paper).

 

4. Feng Luo*, Richard Scheuermann. Detecting Functional Modules from Protein Interaction Networks. Symposium of Computations in Bioinformatics and Bioscience (SCBB06), 123-130, Hangzhou, China, June, 2006.

 

3. Feng Luo, Kun Tang and Latifur Khan. Hierarchical Clustering of Gene Microarray Expression Data. Proc. of Workshop on Clustering High Dimensional Data and its Applications (Conjunction with SDM 2003), 1-10, San Francisco, CA, May 2003.

 

2.  Feng Luo, Kun Tang and Latifur Khan.  Hierarchical Clustering of Gene Expression Data. Proc. of the 3rd IEEE Symposium of Bioinformatics and Bioengineer (BIBE) 2003, Washington DC. 328-335 March 2003.

 

1.  Latifur Khan, Feng Luo. Ontology Construction for Information Selection. Proc. of the 14th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2002), 122-127, Crystal City, Virginia, November 2002.

 

Conference Posts

 

5. Jizhong Zhou, Haichun Gao, Steven D. Brown, Yuri. A. Gorby, Mary S. Lipton, Heather M. Mottaz, Gregory E. Pinchuk, Xiaohu Wang, Yunfeng Yang, Soumitra Barua, Feng Luo, Jianxin Zhong, Xiufeng Wan, Liyou Wu, Dawn Klingeman, Tingfen Yan, Zamin Yang, Christopher Hemme, Josh N. Adkins, Matthew E. Monroe, Eric A. Hill, Christina L. Bilskis, Matthew Fields, Dorothea K. Thompson, Timothy Palzkill, Alex Beliaev, Margaret Romine, Eugene Kolker, Kenneth Nealson, Joel Klappenbach, James M, Tiejde, Richard Smith, Carol Giometti, Margaret Serres, Monica Riley, Lee Ann McCue, James K. Fredrickson. Integrated Analysis of Regulatory Networks Involved in Anaerobic Energy Metabolism of Shewanella oneidensis MR-1. Genomes to Life Contractor-Grantee Workshop II, Department of Energy, Washington, D.C., 2005.

 

4. Feng Luo, Jamie A. Lee, Jennifer Cai, Richard Scheuermann, Identification of Transcription Co-Regulation in B Cell by Integration of Microarray Gene Cluster Classification with Transcription Factor Motif. PSB 2005.

 

3. Feng Luo, Yunfeng Yang, Jizhong Zhou, Richard Scheuermann. Modular Decomposition of Protein Interaction Network. ISMB 2005.

 

2. Burke Squires, Feng Luo, Catherine Spranger, Carey Gire, Jason Lucas, Johanan Lancaon, Kevin Biersack, Richard H. Scheuermann. Elucidating MTB host-pathogen interactions through data integration and analysis utilizing the BioHealthBase Bioinformatics Resource Center. Keystone Symposia, Tuberculosis: Integrating Host and Pathogen Biology, 2005.

 

1. Jizhong Zhou, Dorothea K. Thompson, Matthew W. Fields, Timothy Palzkill, James M. Tiedje, Kenneth H. Nealson, Alex S. Beliaev, Ting Li, Xiufeng Wan, Steven Brown, Dawn Stanek, Weimin Gao, Feng Luo, Jianxin Zhong, Liyou Wu, Barua Soumitra, Crystal B. McAlvin, David Yang, Robert Hettich, Nathan VerBerkmoes, Yuri Gorby, Richard Smith, Mary Lipton, and James Cole. Integrated Analysis of Gene Functions and Regulatory Networks Involved in Anaerobic Energy Metabolism of Shewanella oneidensis MR-1. Genomes to Life Contractor-Grantee Workshop II, Department of Energy, Washington, D.C., 2004.